title: Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis.
abstract: BACKGROUND
  The accuracy of quantitative real-time PCR (qRT-PCR) is highly dependent on reliable reference gene(s). Some housekeeping genes which are commonly used for normalization are widely recognized as inappropriate in many experimental conditions. This study aimed to identify reference genes for clinical studies through microarray meta-analysis of human clinical samples.
  
  
  RESULTS
  After uniform data preprocessing and data quality control, 4,804 Affymetrix HU-133A arrays performed by clinical samples were classified into four physiological states with 13 organ/tissue types. We identified a list of reference genes for each organ/tissue types which exhibited stable expression across physiological states. Furthermore, 102 genes identified as reference gene candidates in multiple organ/tissue types were selected for further analysis. These genes have been frequently identified as housekeeping genes in previous studies, and approximately 71% of them fall into Gene Expression (GO:0010467) category in Gene Ontology.
  
  
  CONCLUSIONS
  Based on microarray meta-analysis of human clinical sample arrays, we identified sets of reference gene candidates for various organ/tissue types and then examined the functions of these genes. Additionally, we found that many of the reference genes are functionally related to transcription, RNA processing and translation. According to our results, researchers could select single or multiple reference gene(s) for normalization of qRT-PCR in clinical studies.
authors.affiliation: Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.
authors.forename: Wei-Chung
authors.initials: WC
authors.lastname: Cheng
authors.forename: Cheng-Wei
authors.initials: CW
authors.lastname: Chang
authors.forename: Chaang-Ray
authors.initials: CR
authors.lastname: Chen
authors.forename: Min-Lung
authors.initials: ML
authors.lastname: Tsai
authors.forename: Wun-Yi
authors.initials: WY
authors.lastname: Shu
authors.forename: Chia-Yang
authors.initials: CY
authors.lastname: Li
authors.forename: Ian C
authors.initials: IC
authors.lastname: Hsu
mesh_terms: D000013:Congenital Abnormalities / Q000235:genetics; D004194:Disease / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards / Q000706:statistics & numerical data; D005796:Genes / Q000502:physiology; D006304:Health Status; D006801:Humans; D008297:Male; D046228:Microarray Analysis / Q000379:methods / Q000592:standards / Q000706:statistics & numerical data; D009369:Neoplasms / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D010829:Physiological Phenomena / Q000235:genetics* / Q000502:physiology; D012015:Reference Standards; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods / Q000592:standards*